5D8T

RNA octamer containing (S)-5' methyl, 2'-F U.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides.

Kel In, A.V.Zlatev, I.Harp, J.Jayaraman, M.Bisbe, A.O Shea, J.Taneja, N.Manoharan, R.M.Khan, S.Charisse, K.Maier, M.A.Egli, M.Rajeev, K.G.Manoharan, M.

(2016) J.Org.Chem. 81: 2261-2279

  • DOI: 10.1021/acs.joc.5b02375
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease ...

    Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease resistance of oligonucleotides (ONs). Here, we report the synthesis of enantiomerically pure (R)- and (S)-5'-C-methyl (C5'-Me) substituted nucleosides and their incorporation into ONs. These modifications generally resulted in a decrease in thermal stability of oligonucleotide (ON) duplexes in a manner dependent on the stereoconfiguration at C5' with greater destabilization characteristic of (R)-epimers. Enhanced stability against snake venom phosphodiesterase resulted from modification of the 3'-end of an ON with either (R)- or (S)-C5'-Me nucleotides. The (S)-isomers with different 2'-substituents provided greater resistance against 3'-exonucleases than the corresponding (R)-isomers. Crystal structure analyses of RNA octamers with (R)- or (S)-5'-C-methyl-2'-deoxy-2'-fluorouridine [(R)- or (S)-C5'-Me-2'-FU, respectively] revealed that the stereochemical orientation of the C5'-Me and the steric effects that emanate from the alkyl substitution are the dominant determinants of thermal stability and are likely molecular origins of resistance against nucleases. X-ray and NMR structural analyses showed that the (S)-C5'-Me epimers are spatially and structurally more similar to their natural 5' nonmethylated counterparts than the corresponding (R)-epimers.


    Organizational Affiliation

    Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA oligonucleotide containing (S)-C5'-Me-2'-FUA,B8synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
A, B
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
U5M
Query on U5M
A, B
RNA linkingC10 H14 F N2 O8 P

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CBV
Query on CBV
A, B
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.120 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 31.172α = 90.00
b = 31.172β = 90.00
c = 84.325γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-08-17 
  • Released Date: 2016-06-29 
  • Deposition Author(s): Harp, J.M., Egli, M.

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Data collection